- Improves test coverage

Author: Alan Christie

.gitignore

@@ -7,6 +7,7 @@
 build
 dist
 *.pyc
+*.tmp
 work
 .nextflow
 .nextflow.log*

src/python/test/pipelines_utils/test_BasicObjectWriter.py

@@ -0,0 +1,55 @@
+import os
+import unittest
+
+from pipelines_utils import BasicObjectWriter
+
+DATA_DIR = os.path.join('test', 'pipelines_utils', 'data')
+
+class BasicObjectWriterTestCase(unittest.TestCase):
+
+    def test_basic_operation_with_supplied_uuid(self):
+        """Test basic file creation.
+        """
+        filename = 'bow_test_a.tmp'
+
+        bow = BasicObjectWriter.BasicObjectWriter(filename)
+        bow.writeHeader()
+        bow.write({"A":"a"}, objectUUID="1234567890")
+        bow.writeFooter()
+        bow.close()
+
+        # Expect something like this: `
+        # [{"uuid": "1234567890", "values": {"A": "a"}}]`
+        #
+        bow_file = open(filename, 'r')
+        line = bow_file.readline()
+        self.assertTrue(line.startswith('[{'))
+        self.assertTrue(line.find('"uuid": "1234567890"') >= 0)
+        self.assertTrue(line.find('"values": {"A": "a"}') >= 0)
+        self.assertTrue(line.endswith('}]'))
+        bow_file.close()
+        os.remove(filename)
+
+    def test_basic_operation_with_generated_uuid(self):
+        """Test basic file creation.
+        """
+        filename = 'bow_test_b.tmp'
+
+        bow = BasicObjectWriter.BasicObjectWriter(filename)
+        # Chec file
+        bow.writeHeader()
+        bow.write({"A":"a"})
+        bow.writeFooter()
+        bow.close()
+
+        # Expect something like this: `
+        # [{"uuid": "1234567890", "values": {"A": "a"}}]`
+        #
+        bow_file = open(filename, 'r')
+        line = bow_file.readline()
+        self.assertTrue(line.startswith('[{'))
+        self.assertTrue(line.find('"uuid": ') >= 0)
+        self.assertTrue(line.find('"values": {"A": "a"}') >= 0)
+        self.assertTrue(line.endswith('}]'))
+        bow_file.close()
+        os.remove(filename)

src/python/test/pipelines_utils/test_TsvWriter.py

@@ -0,0 +1,35 @@
+import os
+import unittest
+
+from collections import OrderedDict
+
+from pipelines_utils import TsvWriter
+
+DATA_DIR = os.path.join('test', 'pipelines_utils', 'data')
+
+class TsvWriterTestCase(unittest.TestCase):
+
+    def test_basic_operation_with_supplied_uuid(self):
+        """Test basic file creation.
+        """
+        filename = 'bow_test_a.tmp'
+        header = OrderedDict()
+        header['a'] = 'one'
+        header['b'] = 'two'
+
+        tw = TsvWriter.TsvWriter(filename, header)
+        tw.writeHeader()
+        tw.write({'a': '123', 'b': '456'})
+        tw.writeFooter()
+        tw.close()
+
+        # Expect something like this: `
+        # [{"uuid": "1234567890", "values": {"A": "a"}}]`
+        #
+        tw_file = open(filename, 'r')
+        line = tw_file.readline()
+        self.assertEquals('one\ttwo\n', line)
+        line = tw_file.readline()
+        self.assertEquals('123\t456\n', line)
+        tw_file.close()
+        os.remove(filename)

src/python/test/pipelines_utils/test_parameter_utils.py

@@ -1,5 +1,7 @@
 import unittest
 
+import argparse
+
 from pipelines_utils import parameter_utils
 
 
@@ -63,3 +65,49 @@ def test_expand_parameters_with_real_data(self):
         a, b, c, d, e, f, g = parameter_utils.expandParameters(t1, t2, t3, t4, t5, t6, t7)
         self.assertEquals([0.135, 0.675, 1.35], a)
         self.assertEquals([0.29, 0.23, 0.23], g)
+
+    def test_add_default_input_args_with_short_options(self):
+        """Checks ArgParse manipulation.
+        """
+        parser = argparse.ArgumentParser()
+
+        parameter_utils.add_default_input_args(parser)
+
+        result = parser.parse_args('-i inputfile -if sdf'.split())
+        self.assertEquals('inputfile', result.input)
+        self.assertEquals('sdf', result.informat)
+
+    def test_add_default_output_args_with_short_options(self):
+        """Checks ArgParse manipulation.
+        """
+        parser = argparse.ArgumentParser()
+
+        parameter_utils.add_default_output_args(parser)
+
+        result = parser.parse_args('-o outputfile -of sdf --meta'.split())
+        self.assertEquals('outputfile', result.output)
+        self.assertEquals('sdf', result.outformat)
+        self.assertTrue(result.meta)
+
+    def test_add_default_input_args_with_long_options(self):
+        """Checks ArgParse manipulation.
+        """
+        parser = argparse.ArgumentParser()
+
+        parameter_utils.add_default_input_args(parser)
+
+        result = parser.parse_args('--input inputfile --informat sdf'.split())
+        self.assertEquals('inputfile', result.input)
+        self.assertEquals('sdf', result.informat)
+
+    def test_add_default_output_args_with_long_options(self):
+        """Checks ArgParse manipulation.
+        """
+        parser = argparse.ArgumentParser()
+
+        parameter_utils.add_default_output_args(parser)
+
+        result = parser.parse_args('--output outputfile --outformat sdf --meta'.split())
+        self.assertEquals('outputfile', result.output)
+        self.assertEquals('sdf', result.outformat)
+        self.assertTrue(result.meta)

src/python/test/pipelines_utils/test_utils.py

@@ -2,7 +2,7 @@
 
 import os
 
-from pipelines_utils import utils
+from pipelines_utils import parameter_utils, utils
 
 
 class UtilsTestCase(unittest.TestCase):
@@ -69,3 +69,37 @@ def test_write_metrics(self):
         os.remove(m_filename)
         self.assertTrue(found_a)
         self.assertTrue(found_b)
+
+    def test_generate_molecule_object_dict_without_values(self):
+        """Checks molecule object creation without values.
+        """
+        source = 'COCC(=O)NC=1C=CC=C(NC(=O)C)C1'
+        format = 'smiles'
+        values = None
+
+        m = utils.generate_molecule_object_dict(source, format, values)
+
+        self.assertEquals(3, len(m))
+        self.assertTrue('uuid' in m)
+        self.assertTrue('source' in m)
+        self.assertTrue('format' in m)
+        self.assertEquals('smiles', m['format'])
+        self.assertEquals(source, m['source'])
+
+    def test_generate_molecule_object_dict_with_values(self):
+        """Checks molecule object creation with values.
+        """
+        source = 'COCC(=O)NC=1C=CC=C(NC(=O)C)C1'
+        format = 'smiles'
+        values = {'a':1}
+
+        m = utils.generate_molecule_object_dict(source, format, values)
+
+        self.assertEquals(4, len(m))
+        self.assertTrue('uuid' in m)
+        self.assertTrue('source' in m)
+        self.assertTrue('format' in m)
+        self.assertTrue('values' in m)
+        self.assertEquals('smiles', m['format'])
+        self.assertEquals(source, m['source'])
+        self.assertEquals(values, m['values'])